Permalinks/htaccess error

Hi everyone, I’m facing a rather frustrating error.

I have an instance of wordpress running for the archives of my organizations publications here.
http://www.dollarsandsense.org/archives.html

The wordpress instance is installed in archives/wp, and I am trying to transition over my old archives into the new system, while maintaining the same url structure for the new posts as i had earlier.

heres a sample of what a normal article looks like in my old system- archives/year/(monthno)(yearno)(authorname)

http://www.dollarsandsense.org/archives/2013/0713pollin.html

At first, i hoped Page Links To plugin would give me what i wanted, but creating posts using those links gives me 404 errors. All posts made using non default permalinks settings also give 404 errors, and even worse, break the old archives (which shouldn’t be affected as it they’re html files unconnected to wordpress other than being in the same folder).

I read that the problem may be related to htaccess file, i’ve tried deleting it and regenerating it with no luck.

I’m a wordpress newbie, so please don’t make your response too technical.